C1qc (complement C1q C chain) - Rat Genome Database

Name: C1qc
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: C1qc (complement C1q C chain) Rattus norvegicus

Analyze

Symbol:

C1qc

Name:

complement C1q C chain

RGD ID:

1306828

Description:

Predicted to be involved in negative regulation of granulocyte differentiation; negative regulation of macrophage differentiation; and synapse pruning. Localizes to synapse. Orthologous to human C1QC (complement C1q C chain); PARTICIPATES IN Chagas disease pathway; coagulation cascade pathway; complement system pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol; 17beta-estradiol 3-benzoate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Also known as:

Adib; adiponectin b; C1qg; complement C1q subcomponent subunit C; complement component 1, q subcomponent, C chain; complement component 1, q subcomponent, gamma polypeptide; LOC362634; MGC105681

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	C1QC (complement C1q C chain)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Mus musculus (house mouse):	C1qc (complement component 1, q subcomponent, C chain)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	C1qc (complement C1q C chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	C1QA (complement C1q A chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	C1QC (complement C1q C chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101960229 (complement C1q subcomponent subunit C)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	C1QC (complement C1q C chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	C1QC (complement C1q C chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	C1qc (complement C1q C chain)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	C1QC (complement C1q C chain)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	C1qc (complement component 1, q subcomponent, C chain)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	149,127,424 - 149,130,732 (-)	NCBI
Rnor_6.0 Ensembl	5	155,255,005 - 155,258,392 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	155,255,013 - 155,258,631 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	159,017,512 - 159,021,130 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	155,656,104 - 155,659,430 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	155,666,143 - 155,669,469 (-)	NCBI
Celera	5	147,525,168 - 147,528,479 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

C1q Deficiency (ISO)

COVID-19 (ISO)

Experimental Liver Cirrhosis (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (EXP)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,6-trinitrobenzenesulfonic acid (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (EXP)

4,4'-sulfonyldiphenol (ISO)

4-amino-2,6-dinitrotoluene (EXP)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

7,12-dimethyltetraphene (ISO)

acetamide (EXP)

acrylamide (EXP)

aflatoxin B1 (EXP,ISO)

amitriptyline (EXP)

antirheumatic drug (ISO)

aristolochic acid (EXP)

benzo[a]pyrene (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

C60 fullerene (EXP)

cadmium atom (ISO)

cadmium dichloride (EXP)

calcitriol (ISO)

captan (ISO)

carbon nanotube (ISO)

copper atom (ISO)

copper(0) (ISO)

cyclosporin A (EXP)

diclofenac (ISO)

disodium selenite (ISO)

diuron (EXP)

doxorubicin (EXP)

endosulfan (EXP)

ethanol (ISO)

flutamide (EXP)

folpet (ISO)

gentamycin (EXP)

indoles (EXP)

ketamine (EXP)

lansoprazole (EXP)

lipopolysaccharide (ISO)

medroxyprogesterone acetate (ISO)

N-nitrosodiethylamine (EXP,ISO)

N-nitrosodimethylamine (EXP)

nickel atom (ISO)

nickel sulfate (ISO)

nimesulide (EXP)

omeprazole (EXP)

paclitaxel (EXP)

pantoprazole (EXP)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

pravastatin (EXP,ISO)

probucol (ISO)

rabeprazole (EXP)

resveratrol (EXP)

silicon dioxide (ISO)

sirolimus (EXP)

Soman (EXP)

streptozocin (EXP)

tacrolimus hydrate (ISO)

testosterone (EXP)

tetrachloromethane (ISO)

titanium dioxide (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (EXP)

troglitazone (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

complement activation, classical pathway (IEA)

innate immune response (IEA)

negative regulation of granulocyte differentiation (IEA,ISO)

negative regulation of macrophage differentiation (IEA,ISO)

synapse pruning (IEA,ISO)

Cellular Component

cellular_component (ND)

collagen trimer (IEA)

extracellular region (IEA)

postsynapse (IEA,ISO)

synapse (IDA,ISO)

Molecular Function

molecular_function (ND)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

Chagas disease pathway (IEA)

coagulation cascade pathway (IEA)

complement system pathway (IEA)

prion disease pathway (IEA)

Staphylococcus aureus infection pathway (IEA)

systemic lupus erythematosus pathway (IEA)

References

References - curated


1.	GOA data from the GO Consortium
2.	MGD data from the GO Consortium
3.	OMIM Disease Annotation Pipeline
4.	Pipeline to import KEGG annotations from KEGG into RGD
5.	RGD automated data pipeline
6.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	RGD automated import pipeline for gene-chemical interactions
8.	RGD comprehensive gene curation
9.	Stevens B, etal., Cell. 2007 Dec 14;131(6):1164-78. doi: 10.1016/j.cell.2007.10.036.

Additional References at PubMed

PMID:8464426	PMID:10961870	PMID:12477932	PMID:15489334	PMID:22516433	PMID:22664934	PMID:23376485	PMID:24006456	PMID:24939307	PMID:25931508	PMID:26316108	PMID:27033548
PMID:29476059

Genomics

Comparative Map Data

C1qc
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	149,127,424 - 149,130,732 (-)	NCBI
Rnor_6.0 Ensembl	5	155,255,005 - 155,258,392 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	5	155,255,013 - 155,258,631 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	5	159,017,512 - 159,021,130 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	155,656,104 - 155,659,430 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	5	155,666,143 - 155,669,469 (-)	NCBI
Celera	5	147,525,168 - 147,528,479 (-)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

C1QC
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	1	22,643,633 - 22,648,110 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	1	22,643,633 - 22,648,108 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	1	22,970,126 - 22,974,601 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	22,842,734 - 22,847,190 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	1	22,715,452 - 22,719,908	NCBI
Celera	1	21,294,833 - 21,299,316 (+)	NCBI
Cytogenetic Map	1	p36.12	NCBI
HuRef	1	21,214,476 - 21,218,943 (+)	NCBI		HuRef
CHM1_1	1	23,082,633 - 23,087,117 (+)	NCBI		CHM1_1

C1qc
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	136,617,112 - 136,620,242 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	4	136,617,115 - 136,620,376 (-)	Ensembl
GRCm38	4	136,889,801 - 136,892,936 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	136,889,804 - 136,893,065 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	136,445,717 - 136,448,829 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	4	136,161,886 - 136,164,949 (-)	NCBI			mm8
Celera	4	135,097,110 - 135,100,232 (-)	NCBI		Celera
Cytogenetic Map	4	D3	NCBI
cM Map	4	69.05	NCBI

C1qc
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955452	2,758,821 - 2,762,522 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955452	2,759,079 - 2,762,522 (+)	NCBI	ChiLan1.0	ChiLan1.0

C1QA
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	1	22,770,557 - 22,773,682 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	1	21,821,927 - 21,825,020 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

C1QC
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	76,660,039 - 76,664,602 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	76,660,035 - 76,664,577 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	73,164,924 - 73,169,492 (-)	NCBI
ROS_Cfam_1.0	2	77,219,290 - 77,223,860 (-)	NCBI
UMICH_Zoey_3.1	2	74,040,178 - 74,044,743 (-)	NCBI
UNSW_CanFamBas_1.0	2	75,048,597 - 75,053,163 (-)	NCBI
UU_Cfam_GSD_1.0	2	76,052,212 - 76,056,780 (-)	NCBI

LOC101960229
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405058	42,188,570 - 42,192,175 (+)	NCBI
SpeTri2.0	NW_004936474	8,013,395 - 8,016,937 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

C1QC
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	80,592,478 - 80,597,459 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	80,592,591 - 80,597,464 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	74,616,498 - 74,621,232 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

C1QC
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	20	110,016,355 - 110,021,123 (-)	NCBI
ChlSab1.1 Ensembl	20	110,016,362 - 110,020,854 (-)	Ensembl

C1qc
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624764	7,369,365 - 7,373,238 (+)	NCBI

Position Markers

RH133915

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	155,255,035 - 155,255,238	NCBI	Rnor6.0
Rnor_5.0	5	159,017,534 - 159,017,737	UniSTS	Rnor5.0
RGSC_v3.4	5	155,656,114 - 155,656,317	UniSTS	RGSC3.4
Celera	5	147,525,178 - 147,525,381	UniSTS
RH 3.4 Map	5	1008.4	UniSTS
Cytogenetic Map	5	q36	UniSTS

AA851367

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	5	155,255,034 - 155,255,233	NCBI	Rnor6.0
Rnor_5.0	5	159,017,533 - 159,017,732	UniSTS	Rnor5.0
RGSC_v3.4	5	155,656,113 - 155,656,312	UniSTS	RGSC3.4
Celera	5	147,525,177 - 147,525,376	UniSTS
RH 3.4 Map	5	1008.8	UniSTS
Cytogenetic Map	5	q36	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	47745646	167946134	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	61612600	168109659	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	71552569	157225114	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	84963058	173504662	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	111278451	156278451	Rat
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	112279412	157279412	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	112279412	157279412	Rat
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	112279412	157279412	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	112279412	157279412	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	112279412	157279412	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	114140832	159140832	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	114140832	159140832	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	116767924	161767924	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	116767924	161767924	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	116767924	161767924	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	116767924	161767924	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	125455818	157225114	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	128687766	173687766	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	131077716	173707219	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132551937	173707219	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	133943857	173707219	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	133943857	173707219	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	134197905	173707219	Rat
70156	Niddm30	Non-insulin dependent diabetes mellitus QTL 30	3.98		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	5	134502140	157212422	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	134712342	173707219	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	134712342	173707219	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	136354114	173707219	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	136640731	173707219	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	138154677	172402610	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	142307322	173707219	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	142309061	173707219	Rat
1331721	Bp210	Blood pressure QTL 210	3.413		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	149029982	173687766	Rat
2302369	Scl60	Serum cholesterol level QTL 60	3.13		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	149568588	167739697	Rat
631263	Cm24	Cardiac mass QTL 24	3.5		heart mass (VT:0007028)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	149832180	164807402	Rat
1300119	Bp180	Blood pressure QTL 180	3.82		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	150340838	164298744	Rat
2313096	Bmd78	Bone mineral density QTL 78	3.1	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	5	150360936	167946134	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	59
Count of miRNA genes:	45
Interacting mature miRNAs:	56
Transcripts:	ENSRNOT00000017065
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	33	53	37	19	37	8	11	62	28	33	11	8
Low		8	4	4		4			12	7	8
Below cutoff		2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008524	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006239225	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC113790	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC086409	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ218827	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219610	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220269	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228978	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	LT963068	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000017065 ⟹ ENSRNOP00000017065

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	5	155,255,005 - 155,258,392 (-)	Ensembl

RefSeq Acc Id:

NM_001008524 ⟹ NP_001008524

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	149,127,424 - 149,130,732 (-)	NCBI
Rnor_6.0	5	155,255,025 - 155,258,351 (-)	NCBI
Rnor_5.0	5	159,017,512 - 159,021,130 (-)	NCBI
RGSC_v3.4	5	155,656,104 - 155,659,430 (-)	RGD
Celera	5	147,525,168 - 147,528,479 (-)	RGD

Sequence:

show sequence

GCCTGAAGTCCCCTACATGCTCAGGATGGTTGTAGGAACCAGCTGCCAGCCCCAGCATGGACTC
TACCTGCTGCTGCTCCTTCTGGCCCTACCCCTCAGGAGCCAGGCCAACGCTGGCTGCTATGGGA
TCCCAGGGATGCCAGGCCTGCCGGGAACCCCTGGGAAGGATGGGCATGATGGACTTCAGGGGCC
CAAGGGTGAGCCGGGAATCCCAGCCATCCCTGGGACACAAGGACCCAAGGGTCAGAAGGGCGAG
CCGGGTATGCCTGGCCATCGTGGGAAAAACGGCCCCATGGGGACCTCTGGGTCGCCAGGGGATC
CAGGCCCCAGGGGTCCTCCCGGGGAGCCGGGTGAGGAGGGTCGATACAAACAGAAGCATCAGTC
GGTGTTCACGGTCACCCGGCAGACCGCGCAGTACCCAGCGGCCAATGGCCTTGTCAAGTTCAAT
TCCGCCATCACCAATCCTCAGGGGGATTACAACACAAACACGGGGAAGTTCACCTGCAAAGTGC
CCGGCCTCTACTACTTCGTCCACCACACATCCCAGACGGCCAACCTGTGCGTGCAGCTGCTCCT
CAACAATGCCAAGGTGACCAGCTTCTGCGACCACATGTCCAACAGCAAGCAGGTCAGCTCAGGA
GGAGTACTCCTGCGGCTGCAGAGGGGCGACGAGGTGTGGCTGGCCGTCAACGACTACAACGGCA
TGGTGGGCACTGAGGGCTCTGACAGCGTCTTCTCTGGTTTCCTACTGTTTCCTGACTAGAATGG
CAGGCTGGGTCCAGCACCCGGACGCCCGCCTCGCTCCCTCTGCTTTCCCCATCCTCACTCAGAC
CTCTTCCTTCAGGAAGTCCACCCTGGTTCCTGACCCATCAGCCCTCTGTCTCCTCAGAGTTTCT
CTGGGAATCACTGACTGGTTCCATTCCAGTGGCAGTTTATCGAGACCTTTATGAGACTATTTTT
TTTTCAGGTGGGAAGAGAGAAAAATAAATAGATCACTAAATAAATATGCCTGGCCCAGATTTCT
CACTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006239225 ⟹ XP_006239287

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	155,255,013 - 155,258,631 (-)	NCBI
Rnor_5.0	5	159,017,512 - 159,021,130 (-)	NCBI

Sequence:

show sequence

CACATCCTGGTGTTCCCAGGATGAAGGGACAGCAGGCACTTCCTCATTTAGACACACATGACCT
AGGGCCAGGGAAGGAAGGGGTGGACAGAGGTGTCACTGTGGTCAGCCTGGCTCAGAACCTAAAA
GAAAGTGTCAAGTCAGGGAAAATTTCTGGAAAGGGGATGTGGGATTAGGGTGCTGTGGGGGAGG
GGAGGGGCCCCTGCTCTGGGCGGCTCTTCTCTGACCACTCTGAAACAGTGTCTTCCTGTCTGGG
AGAACAGGACGTCTCTCTGATTAGGCCTGAAGTCCCCTACATGCTCAGGATGGTTGTAGGAACC
AGCTGCCAGCCCCAGCATGGACTCTACCTGCTGCTGCTCCTTCTGGCCCTACCCCTCAGGAGCC
AGGCCAACGCTGGCTGCTATGGGATCCCAGGGATGCCAGGCCTGCCGGGAACCCCTGGGAAGGA
TGGGCATGATGGACTTCAGGGGCCCAAGGGTGAGCCGGGAATCCCAGCCATCCCTGGGACACAA
GGACCCAAGGGTCAGAAGGGCGAGCCGGGTATGCCTGGCCATCGTGGGAAAAACGGCCCCATGG
GGACCTCTGGGTCGCCAGGGGATCCAGGCCCCAGGGGTCCTCCCGGGGAGCCGGGTGAGGAGGG
TCGATACAAACAGAAGCATCAGTCGGTGTTCACGGTCACCCGGCAGACCGCGCAGTACCCAGCG
GCCAATGGCCTTGTCAAGTTCAATTCCGCCATCACCAATCCTCAGGGGGATTACAACACAAACA
CGGGGAAGTTCACCTGCAAAGTGCCCGGCCTCTACTACTTCGTCCACCACACATCCCAGACGGC
CAACCTGTGCGTGCAGCTGCTCCTCAACAATGCCAAGGTGACCAGCTTCTGCGACCACATGTCC
AACAGCAAGCAGGTCAGCTCAGGAGGAGTACTCCTGCGGCTGCAGAGGGGCGACGAGGTGTGGC
TGGCCGTCAACGACTACAACGGCATGGTGGGCACTGAGGGCTCTGACAGCGTCTTCTCTGGTTT
CCTACTGTTTCCTGACTAGAATGGCAGGCTGGGTCCAGCACCCGGACGCCCGCCTCGCTCCCTC
TGCTTTCCCCATCCTCACTCAGACCTCTTCCTTCAGGAAGTCCACCCTGGTTCCTGACCCATCA
GCCCTCTGTCTCCTCAGAGTTTCTCTGGGAATCACTGACTGGTTCCATTCCAGTGGCAGTTTAT
CGAGACCTTTATGAGACTATTTTTTTTTCAGGTGGGAAGAGAGAAAAATAAATAGATCACTAAA
TAAATATGCCTGGCCCAGATTTCTCACTAGAAGGCCTCAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001008524	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH86409	(Get FASTA)	NCBI Sequence Viewer
	EDL80826	(Get FASTA)	NCBI Sequence Viewer
	P31722	(Get FASTA)	NCBI Sequence Viewer
	SOR70286	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001008524 ⟸ NM_001008524
- Peptide Label:	precursor
- UniProtKB:	P31722 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MVVGTSCQPQHGLYLLLLLLALPLRSQANAGCYGIPGMPGLPGTPGKDGHDGLQGPKGEPGIPA IPGTQGPKGQKGEPGMPGHRGKNGPMGTSGSPGDPGPRGPPGEPGEEGRYKQKHQSVFTVTRQT AQYPAANGLVKFNSAITNPQGDYNTNTGKFTCKVPGLYYFVHHTSQTANLCVQLLLNNAKVTSF CDHMSNSKQVSSGGVLLRLQRGDEVWLAVNDYNGMVGTEGSDSVFSGFLLFPD hide sequence

RefSeq Acc Id:

XP_006239287 ⟸ XM_006239225

- Peptide Label:

isoform X1

- Sequence:

show sequence

MLRMVVGTSCQPQHGLYLLLLLLALPLRSQANAGCYGIPGMPGLPGTPGKDGHDGLQGPKGEPG
IPAIPGTQGPKGQKGEPGMPGHRGKNGPMGTSGSPGDPGPRGPPGEPGEEGRYKQKHQSVFTVT
RQTAQYPAANGLVKFNSAITNPQGDYNTNTGKFTCKVPGLYYFVHHTSQTANLCVQLLLNNAKV
TSFCDHMSNSKQVSSGGVLLRLQRGDEVWLAVNDYNGMVGTEGSDSVFSGFLLFPD

hide sequence

RefSeq Acc Id:

ENSRNOP00000017065 ⟸ ENSRNOT00000017065

Protein Domains

C1q Collagen-like

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13694174

Promoter ID:

EPDNEW_R4699

Type:

initiation region

Name:

C1qc_1

Description:

complement C1q C chain

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	5	155,258,398 - 155,258,458	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306828	AgrOrtholog
Ensembl Genes	ENSRNOG00000012804	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000017065	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000017065	UniProtKB/TrEMBL
Gene3D-CATH	2.60.120.40	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7306579	IMAGE-MGC_LOAD
InterPro	C1q_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Collagen	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tumour_necrosis_fac-like_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:362634	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:105681	IMAGE-MGC_LOAD
NCBI Gene	362634	ENTREZGENE
Pfam	C1q	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Collagen	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	C1qc	PhenoGen
PRINTS	COMPLEMNTC1Q	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	C1Q	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	C1Q	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49842	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0H2UHK1_RAT	UniProtKB/TrEMBL
	C1QC_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	Q5RJZ8	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-07-13	C1qc	complement C1q C chain	C1qc	complement component 1, q subcomponent, C chain	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-03	C1qc	complement component 1, q subcomponent, C chain	C1qg	complement component 1, q subcomponent, gamma polypeptide	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-12-06	C1qg	complement component 1, q subcomponent, gamma polypeptide	C1qg_predicted	complement component 1, q subcomponent, gamma polypeptide (predicted)	Symbol and Name updated	1559027	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)